Pipeline does not run through GATK step

[KristinaGagalova]

Description of the bug

Hi,
I am running rnavar on a non-model organims species and I don't have vcf annotations or calibration for it. The pipeline runs after the mapping stage and it does not go to GATK.

executor >  slurm (47)
[12/1cec80] process > NFCORE_RNAVAR:RNAVAR:PREPAR... [100%] 1 of 1 ✔
[cf/96eccc] process > NFCORE_RNAVAR:RNAVAR:PREPAR... [100%] 1 of 1 ✔
[e0/4dab2d] process > NFCORE_RNAVAR:RNAVAR:PREPAR... [100%] 1 of 1 ✔
[6c/e28e84] process > NFCORE_RNAVAR:RNAVAR:INPUT_... [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNAVAR:RNAVAR:CAT_FASTQ -
[a7/e9c640] process > NFCORE_RNAVAR:RNAVAR:FASTQC... [100%] 1 of 1 ✔
[c4/617bf4] process > NFCORE_RNAVAR:RNAVAR:GATK4_... [100%] 1 of 1 ✔
[86/e568e0] process > NFCORE_RNAVAR:RNAVAR:GATK4_... [100%] 1 of 1 ✔
[80/111ba2] process > NFCORE_RNAVAR:RNAVAR:ALIGN_... [100%] 1 of 1 ✔
[23/1ca68d] process > NFCORE_RNAVAR:RNAVAR:ALIGN_... [100%] 1 of 1 ✔
[41/8ad986] process > NFCORE_RNAVAR:RNAVAR:ALIGN_... [100%] 1 of 1 ✔
[31/af1859] process > NFCORE_RNAVAR:RNAVAR:ALIGN_... [100%] 1 of 1 ✔
[b5/88a156] process > NFCORE_RNAVAR:RNAVAR:ALIGN_... [100%] 1 of 1 ✔
[c6/67b710] process > NFCORE_RNAVAR:RNAVAR:ALIGN_... [100%] 1 of 1 ✔
[02/99c6a2] process > NFCORE_RNAVAR:RNAVAR:MARKDU... [100%] 1 of 1 ✔
[0d/cc7179] process > NFCORE_RNAVAR:RNAVAR:MARKDU... [100%] 1 of 1 ✔
[0b/0e79a5] process > NFCORE_RNAVAR:RNAVAR:MARKDU... [100%] 1 of 1 ✔
[52/13a903] process > NFCORE_RNAVAR:RNAVAR:MARKDU... [100%] 1 of 1 ✔
[c2/d94ff1] process > NFCORE_RNAVAR:RNAVAR:MARKDU... [100%] 1 of 1 ✔
[79/a55ab1] process > NFCORE_RNAVAR:RNAVAR:SPLITN... [100%] 25 of 25 ✔
[c9/7186bd] process > NFCORE_RNAVAR:RNAVAR:SPLITN... [100%] 1 of 1 ✔
[e9/bfc666] process > NFCORE_RNAVAR:RNAVAR:SPLITN... [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNAVAR:RNAVAR:GATK4_... -
[-        ] process > NFCORE_RNAVAR:RNAVAR:RECALI... -
[-        ] process > NFCORE_RNAVAR:RNAVAR:RECALI... -
[-        ] process > NFCORE_RNAVAR:RNAVAR:RECALI... -
[-        ] process > NFCORE_RNAVAR:RNAVAR:GATK4_... -
[-        ] process > NFCORE_RNAVAR:RNAVAR:GATK4_... -
[-        ] process > NFCORE_RNAVAR:RNAVAR:TABIX     -
[-        ] process > NFCORE_RNAVAR:RNAVAR:GATK4_... -
[fd/c277a2] process > NFCORE_RNAVAR:RNAVAR:CUSTOM... [100%] 1 of 1 ✔
[b5/b3074a] process > NFCORE_RNAVAR:RNAVAR:MULTIQC   [100%] 1 of 1 ✔
-[nf-core/rnavar] Pipeline completed successfully-

Could you please advise on what I may have done wrong? I included a mock vcf for the snps db.

Command used and terminal output

nextflow run ./main.nf \
        -resume \
        -profile singularity,pawsey_setonix \
        --input samples.csv \
        --fasta "/path/to/genome/genome.fna" \
        --gtf "/path/to/genome/genome.gtf" \
        --star_index "/path/to/genome/star_index" \
        --dbsnp "/path/to/rnavar/mockdb.vcf" \
        --skip-basecalibration true \
        --skip_variantannotation true

Relevant files

No response

System information

module load nextflow/23.10.0
module load singularity/4.1.0-slurm
Launching ./main.nf [reverent_mcclintock] DSL2 - revision: e58604470a

[ERIGR]

Hi, I have exactly the same problem than Kristina. Of note, read length for me was of 100 bp. Could you specify precise settings in this case that works for 100 bp reads ? For example which genome files should I use (fasta files and gtf files). Which one should I use GRCh38 (and from NCBI, ensembl or GATK ?) or hg38 ? Where should I download these files to be sure that it will works ?
Using -- genome GRCh38 doesn't work for me. Problems occur always at the GATK stage after the mapping.

Thanks for your advices.

[KristinaGagalova]

@ERIGR It works on the dev branch for me. Since I have a non-model species, I added --skip_baserecalibration true; for the rest I run it with default like this:

nextflow run ./main.nf \
        -resume \
        -profile singularity,pawsey_setonix \
        --input samples.csv \
        --fasta "/path/to/genome/genome.fna" \
        --gtf "/path/to/genome/genome.gtf" \
        --star_index "/path/to/genome/star_index" \
        --skip_baserecalibration true